data_DFX
#
_chem_comp.id DFX
_chem_comp.name 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula 'C5 H9 F O3'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 136.122
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DFX
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1BVV
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id DFX
_pdbx_chem_comp_synonyms.name 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
DFX C1 C1 C 0 1 N N N N N N 32.825 21.620 35.045 -1.065 1.481 0.173 C1 DFX 1
DFX C2 C2 C 0 1 N N S N N N 32.938 20.726 36.299 -1.215 0.030 -0.290 C2 DFX 2
DFX C3 C3 C 0 1 N N S N N N 33.532 21.505 37.480 -0.026 -0.788 0.223 C3 DFX 3
DFX C4 C4 C 0 1 N N R N N N 34.808 22.290 37.100 1.273 -0.149 -0.278 C4 DFX 4
DFX C5 C5 C 0 1 N N N N N N 35.244 22.046 35.629 1.327 1.310 0.184 C5 DFX 5
DFX O3 O3 O 0 1 N N N N N N 33.816 20.605 38.544 -0.120 -2.127 -0.265 O3 DFX 6
DFX O4 O4 O 0 1 N N N N N N 34.572 23.680 37.296 2.392 -0.860 0.254 O4 DFX 7
DFX O5 O5 O 0 1 N N N N N N 34.125 22.149 34.693 0.177 2.005 -0.302 O5 DFX 8
DFX F2 F2 F 0 1 N N N N N N 31.674 20.193 36.668 -2.404 -0.503 0.221 F2 DFX 9
DFX H1 H11 H 0 1 N N N N N N 32.437 21.022 34.207 -1.887 2.077 -0.225 H1 DFX 10
DFX H12 H12 H 0 1 N N N N N N 32.142 22.455 35.258 -1.083 1.519 1.262 H12 DFX 11
DFX H2 H2 H 0 1 N N N N N N 33.611 19.894 36.045 -1.238 -0.005 -1.379 H2 DFX 12
DFX H3 H3 H 0 1 N N N N N N 32.783 22.247 37.794 -0.031 -0.794 1.314 H3 DFX 13
DFX H4 H4 H 0 1 N N N N N N 35.623 21.933 37.746 1.300 -0.187 -1.367 H4 DFX 14
DFX H51 H51 H 0 1 N N N N N N 35.997 22.801 35.358 1.340 1.345 1.273 H51 DFX 15
DFX H52 H52 H 0 1 N N N N N N 35.648 21.025 35.561 2.229 1.781 -0.207 H52 DFX 16
DFX HO3 HO3 H 0 1 N N N N N N 33.879 19.721 38.203 -0.923 -2.590 0.009 HO3 DFX 17
DFX HO4 HO4 H 0 1 N N N N N N 34.519 23.865 38.226 3.249 -0.510 -0.023 HO4 DFX 18
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
DFX C1 C2 SING N N 1
DFX C1 O5 SING N N 2
DFX C1 H1 SING N N 3
DFX C1 H12 SING N N 4
DFX C2 C3 SING N N 5
DFX C2 F2 SING N N 6
DFX C2 H2 SING N N 7
DFX C3 C4 SING N N 8
DFX C3 O3 SING N N 9
DFX C3 H3 SING N N 10
DFX C4 C5 SING N N 11
DFX C4 O4 SING N N 12
DFX C4 H4 SING N N 13
DFX C5 O5 SING N N 14
DFX C5 H51 SING N N 15
DFX C5 H52 SING N N 16
DFX O3 HO3 SING N N 17
DFX O4 HO4 SING N N 18
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
DFX SMILES ACDLabs 10.04 'FC1COCC(O)C1O'
DFX SMILES_CANONICAL CACTVS 3.341 'O[C@@H]1COC[C@H](F)[C@H]1O'
DFX SMILES CACTVS 3.341 'O[CH]1COC[CH](F)[CH]1O'
DFX SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C1[C@H]([C@@H]([C@H](CO1)F)O)O'
DFX SMILES 'OpenEye OEToolkits' 1.5.0 'C1C(C(C(CO1)F)O)O'
DFX InChI InChI 1.03 'InChI=1S/C5H9FO3/c6-3-1-9-2-4(7)5(3)8/h3-5,7-8H,1-2H2/t3-,4+,5+/m0/s1'
DFX InChIKey InChI 1.03 YIJTWYXBSRZXRS-VPENINKCSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
DFX 'SYSTEMATIC NAME' ACDLabs 10.04 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol
DFX 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(3R,4S,5S)-5-fluorooxane-3,4-diol'
DFX 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 D-1-deoxy-Xylp2fluoro
#
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
DFX 'CARBOHYDRATE ISOMER' D PDB ?
DFX 'CARBOHYDRATE RING' pyranose PDB ?
DFX 'CARBOHYDRATE PRIMARY CARBONYL GROUP' aldose PDB ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DFX 'Create component' 1999-07-08 EBI
DFX 'Modify descriptor' 2011-06-04 RCSB
DFX 'Other modification' 2020-07-03 RCSB
DFX 'Modify name' 2020-07-17 RCSB
DFX 'Modify synonyms' 2020-07-17 RCSB
DFX 'Modify linking type' 2020-07-17 RCSB
DFX 'Modify atom id' 2020-07-17 RCSB
DFX 'Modify component atom id' 2020-07-17 RCSB
DFX 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 DFX GLU None Carbohydrate 'Amino-acid side chain' 'Any position' C1 OE1 ? ?
2 DFX GLU None Carbohydrate 'Amino-acid side chain' 'Any position' C1 OE2 ? ?
#
_pdbe_chem_comp_synonyms.comp_id DFX
_pdbe_chem_comp_synonyms.name 1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
DFX C1 C 5.104 -1.732 1
DFX C2 C 5.104 -0.233 2
DFX C3 C 6.404 0.517 3
DFX C4 C 7.702 -0.233 4
DFX C5 C 7.702 -1.732 5
DFX O3 O 6.404 2.018 6
DFX O4 O 9.002 0.517 7
DFX O5 O 6.404 -2.482 8
DFX F2 F 3.805 0.517 9
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
DFX C1 C2 SINGLE NONE 1
DFX C1 O5 SINGLE NONE 2
DFX C2 C3 SINGLE NONE 3
DFX C2 F2 SINGLE BEGINDASH 4
DFX C3 C4 SINGLE NONE 5
DFX C3 O3 SINGLE BEGINWEDGE 6
DFX C4 C5 SINGLE NONE 7
DFX C4 O4 SINGLE BEGINDASH 8
DFX C5 O5 SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id DFX
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1CCOCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2
_pdbe_chem_comp_substructure.substructure_inchikeys DHXVGJBLRPWPCS-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
DFX C1 S1 1
DFX C2 S1 1
DFX C3 S1 1
DFX C4 S1 1
DFX C5 S1 1
DFX O5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DFX
_pdbe_chem_comp_rdkit_properties.exactmw 136.054
_pdbe_chem_comp_rdkit_properties.amw 136.122
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 64.879
_pdbe_chem_comp_rdkit_properties.tpsa 49.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.923
_pdbe_chem_comp_rdkit_properties.CrippenMR 27.729
_pdbe_chem_comp_rdkit_properties.chi0v 4.103
_pdbe_chem_comp_rdkit_properties.chi1v 2.005
_pdbe_chem_comp_rdkit_properties.chi2v 0.690
_pdbe_chem_comp_rdkit_properties.chi3v 0.690
_pdbe_chem_comp_rdkit_properties.chi4v 0.309
_pdbe_chem_comp_rdkit_properties.chi0n 13.103
_pdbe_chem_comp_rdkit_properties.chi1n 6.322
_pdbe_chem_comp_rdkit_properties.chi2n 0.690
_pdbe_chem_comp_rdkit_properties.chi3n 0.690
_pdbe_chem_comp_rdkit_properties.chi4n 0.309
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.190
_pdbe_chem_comp_rdkit_properties.kappa1 1.694
_pdbe_chem_comp_rdkit_properties.kappa2 2.597
_pdbe_chem_comp_rdkit_properties.kappa3 1.382
_pdbe_chem_comp_rdkit_properties.Phi 0.489
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
DFX UniChem ZINC ZINC000015297146
DFX UniChem PubChem 5288048
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
DFX C1 1.596 -0.919 -0.024 ETKDGv3 1
DFX C2 1.334 0.520 -0.485 ETKDGv3 2
DFX C3 0.018 1.032 0.113 ETKDGv3 3
DFX C4 -1.109 0.018 -0.154 ETKDGv3 4
DFX C5 -0.654 -1.387 0.282 ETKDGv3 5
DFX O3 -0.300 2.272 -0.464 ETKDGv3 6
DFX O4 -2.256 0.393 0.562 ETKDGv3 7
DFX O5 0.528 -1.770 -0.397 ETKDGv3 8
DFX F2 2.379 1.334 -0.084 ETKDGv3 9
DFX H1 2.522 -1.285 -0.516 ETKDGv3 10
DFX H12 1.775 -0.957 1.075 ETKDGv3 11
DFX H2 1.274 0.540 -1.596 ETKDGv3 12
DFX H3 0.156 1.150 1.215 ETKDGv3 13
DFX H4 -1.329 0.006 -1.248 ETKDGv3 14
DFX H51 -1.453 -2.115 0.025 ETKDGv3 15
DFX H52 -0.515 -1.434 1.387 ETKDGv3 16
DFX HO3 -0.950 2.713 0.143 ETKDGv3 17
DFX HO4 -3.016 -0.110 0.168 ETKDGv3 18
#